Story

In the year 2099, Alchemax is in danger of being taken over by Stark-Fujikawa Industries. However, Walker Sloan, employee and scientist at Alchemax, has devised a plan to save the company. His plan is to travel to the past, launch Alchemax years before it was originally founded, form Alchemax in his own image, and dismantle Stark-Fujikawa Industries before it is even started. When Sloan launches his plan, Spider-Man 2099 arrives and jumps into the time portal in an attempt to stop Sloan from commencing with his plans, but he doesn't succeed.

Once Spider-Man 2099 returns back to 2099, he realizes that Nueva York has changed drastically. Spider-Man 2099 then uses Peter Parker's DNA in Alchemax's archives to create a chronal-link and contact him. He tries to warn Peter, who now worked for the genetics department of Alchemax, of his impending death. However, Peter did not listen to him, stating that he wasn't going to leave if innocent people were in danger. Spider-Man then goes up to the 66th floor of the Alchemax building, battles Anti-Venom, and is defeated. Spider-Man 2099 then uses the portal to retrieve Parker, and bring him back to the future, in an attempt to save his life.

As events unfold, Mary Jane Watson almost dies in the Alchemax building, but is saved by Spider-Man 2099. In the future, Spider-Man learns that he becomes the CEO of Alchemax. His future-self explains that he was able to live so long due to an anti-aging drug Alchemax had developed, and that he had began to seek power after the day he lost everyone he loved. As the CEO tries to explain more to his past-self, Spider-Man leaves to assist Spider-Man 2099 in stabilizing the portal.

After the Spider-Men defeated each others respective villain, the changes to made by Sloan's plot were reversed.

Gameplay

The game uses a "cause and effect" mechanism called Quantum Causality; the decisions Spider-Man makes effects Spider-Man 2099. For example, when Anti-Venom tried to kill Spider-Man with an elevator, the elevator Spider-Man 2099 was in turned into a closet.

Notes

This is the first Spider-Man game to feature Eddie Brock as Anti-Venom.

Peter seems to have organic web-shooters in this game.

Trivia

If players pre-order the game from Gamestop, they will be able to download all four costumes Spider-Man wore in the Identity Crisis story arc (Dusk, Prodigy, Hornet, and Ricochet) as alternate costumes, each providing a boost in a certain attribute.

Peter's Spider-Man costume retains noticeable damage as the game progresses. At one point his ear and hair are visible. (Miguel's Spider-man costume doesn't show any damage because it's made of Unstable Molecule fabric)

J Jonah Jameson mentions a Spider-Man musical during one of his rants about Spider-Man, to which Peter responds; "I'd pay to see that".

Peter Parker tells Miguel O'hara during their initial conversation that he should play a video game, if he wants a Spider-Man that will do what he says. This is ironic as he is in a video game.

This game can be considered a sequel to Spider-Man: Shattered Dimensions due Peter asks if "The other me's are in his head too?", which is a reference to that game.

The entire game takes place inside of the Alchemax building (in both times).

In the Alchemax building in Peter Parker's time, there are a number of outside references mentioned by the PA system, such as "Ben Grimm Airlines" (whether this means his exposure to cosmic rays never happened, he was cured by Alchemax or went solo is unclear), Cain Marko and Matt Murdock (who is still a lawyer in that timeline).

In the personal archives, there are many of the costumes that Spider-Man has used in the past (other than his usual costume), including both Spider-Armors (the MK 1, likely being a recreation of the original, as that was destroyed by acid), Stealth Suit, Future Fondation Suit and a recreation of the Iron Spider suit.

The statues in the personal archives and in the room where Black Cat 2099 is first fought are of Mysterio, Juggernaut, Kraven and Silver Sable, all four of them fought against Spider-Man in Spider-Man: Shattered Dimensions (Silver Sable was just there to command the "minion"-type enemies as Juggernaut doesn't have them).

Both Spider-Men are seen unmasked in this game (mostly in cutscenes).

In the timeline, when Alchemax was founded in the 1970's, Doctor Otto Octavius never turned to crime, but worked for Alchemax instead (with Peter Parker working under him in Alchemax's genetics department), although he still used his tentacles in his work.